Zinc in PDB 3qw1: Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks

The structure of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks, PDB code: 3qw1 was solved by E.N.Salgado, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.20 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.298, 61.843, 70.087, 90.00, 102.22, 90.00
R / Rfree (%)	28.8 / 31.8

The structure of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks (pdb code 3qw1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks, PDB code: 3qw1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:15.2 occ:1.00 NE2 A:HIS77 1.9 15.0 1.0 NE2 D:HIS63 2.0 19.1 1.0 OD2 C:ASP74 2.0 16.0 1.0 NE2 A:HIS73 2.1 13.0 1.0 CD2 D:HIS63 2.8 18.1 1.0 CE1 A:HIS77 2.8 15.6 1.0 CE1 A:HIS73 3.0 11.9 1.0 CG C:ASP74 3.0 15.6 1.0 CD2 A:HIS77 3.0 15.8 1.0 CD2 A:HIS73 3.1 11.7 1.0 CE1 D:HIS63 3.2 19.3 1.0 OD1 C:ASP74 3.3 16.1 1.0 O C:HOH107 4.0 21.8 1.0 ND1 A:HIS77 4.0 15.5 1.0 CG D:HIS63 4.0 18.1 1.0 CG A:HIS77 4.1 16.8 1.0 ND1 A:HIS73 4.1 12.7 1.0 ND1 D:HIS63 4.2 18.7 1.0 CG A:HIS73 4.2 13.1 1.0 CB C:ASP74 4.4 14.3 1.0 CD1 D:ILE67 4.7 8.0 1.0 O C:ASP74 4.9 14.9 1.0 CA C:ASP74 5.0 14.3 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:10.4 occ:1.00 NE2 B:HIS73 2.0 13.2 1.0 NE2 B:HIS77 2.0 15.3 1.0 NE2 C:HIS63 2.1 19.1 1.0 OD2 D:ASP74 2.1 16.5 1.0 OD1 D:ASP74 2.5 15.8 1.0 CG D:ASP74 2.6 15.5 1.0 CE1 B:HIS73 2.9 11.8 1.0 CD2 C:HIS63 2.9 18.0 1.0 CE1 B:HIS77 3.0 15.9 1.0 CD2 B:HIS73 3.0 12.0 1.0 CD2 B:HIS77 3.1 15.9 1.0 CE1 C:HIS63 3.1 19.3 1.0 ND1 B:HIS73 4.0 12.9 1.0 CB D:ASP74 4.1 14.3 1.0 ND1 B:HIS77 4.1 15.5 1.0 CG C:HIS63 4.1 18.1 1.0 CG B:HIS73 4.1 13.3 1.0 ND1 C:HIS63 4.2 18.5 1.0 CG B:HIS77 4.2 16.7 1.0 CD1 C:ILE67 4.6 7.8 1.0 CA D:ASP74 4.8 14.4 1.0 O D:ASP74 4.8 14.9 1.0 CD2 D:LEU78 4.9 16.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:16.1 occ:1.00 NE2 C:HIS77 1.9 15.0 1.0 NE2 B:HIS63 2.0 19.2 1.0 OD2 A:ASP74 2.1 16.6 1.0 NE2 C:HIS73 2.1 13.0 1.0 OD1 A:ASP74 2.6 15.9 1.0 CG A:ASP74 2.7 15.7 1.0 CE1 C:HIS77 2.8 15.8 1.0 CD2 C:HIS77 2.9 15.8 1.0 CD2 B:HIS63 3.0 18.2 1.0 CE1 B:HIS63 3.0 19.2 1.0 CE1 C:HIS73 3.0 11.8 1.0 CD2 C:HIS73 3.1 12.1 1.0 ND1 C:HIS77 3.9 15.7 1.0 CG C:HIS77 4.0 16.8 1.0 ND1 B:HIS63 4.1 18.6 1.0 CG B:HIS63 4.1 18.0 1.0 CB A:ASP74 4.2 14.5 1.0 ND1 C:HIS73 4.2 12.2 1.0 CG C:HIS73 4.2 13.2 1.0 CD1 B:ILE67 4.6 7.9 1.0 O C:HOH107 4.6 21.8 1.0 CD2 A:LEU78 4.7 16.4 1.0 CA A:ASP74 4.8 14.3 1.0 O A:ASP74 4.9 15.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:17.3 occ:1.00 NE2 D:HIS73 2.0 13.0 1.0 NE2 D:HIS77 2.0 15.1 1.0 NE2 A:HIS63 2.1 19.3 1.0 OD2 B:ASP74 2.1 16.6 1.0 CE1 D:HIS73 2.8 11.5 1.0 CG B:ASP74 2.9 15.5 1.0 CD2 A:HIS63 2.9 18.3 1.0 CE1 D:HIS77 3.0 15.8 1.0 CD2 D:HIS77 3.0 15.6 1.0 CD2 D:HIS73 3.1 12.1 1.0 OD1 B:ASP74 3.1 15.9 1.0 CE1 A:HIS63 3.2 19.3 1.0 ND1 D:HIS73 4.0 12.2 1.0 ND1 D:HIS77 4.1 15.3 1.0 CG D:HIS77 4.1 16.8 1.0 CG A:HIS63 4.1 18.2 1.0 CG D:HIS73 4.1 13.4 1.0 ND1 A:HIS63 4.2 18.7 1.0 CB B:ASP74 4.3 14.4 1.0 CD1 A:ILE67 4.6 8.0 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmh Crosslinks within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn107 b:45.3 occ:1.00 OE2 D:GLU4 2.3 52.9 1.0 OD2 D:ASP5 2.5 41.5 1.0 O D:HOH110 2.6 8.9 1.0 O D:HOH111 2.9 12.5 1.0 CD D:GLU4 3.3 51.3 1.0 CG D:ASP5 3.4 39.9 1.0 CB D:ASP5 3.6 38.1 1.0 CG D:GLU4 3.7 46.5 1.0 OE2 D:GLU8 4.2 44.5 1.0 OE1 D:GLU8 4.2 44.0 1.0 OE1 D:GLU4 4.4 52.3 1.0 OD1 D:ASP5 4.5 40.7 1.0 O D:GLU4 4.6 40.0 1.0 CD D:GLU8 4.6 42.6 1.0 CA D:ASP5 4.9 38.0 1.0 C D:GLU4 5.0 40.0 1.0

E.N.Salgado, J.D.Brodin, M.M.To, F.A.Tezcan. Templated Construction of A Zn-Selective Protein Dimerization Motif. Inorg.Chem. V. 50 6323 2011.
ISSN: ISSN 0020-1669
PubMed: 21648390
DOI: 10.1021/IC200746M